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Kinetics of charge transfer in DNA containing a mismatch.

Osakada Y, Kawai K, Fujitsuka M, Majima T - Nucleic Acids Res. (2008)

Bottom Line: While the single-base mismatch would significantly affect the CT in DNA, the kinetic basis for the drastic decrease in the CT efficiency through DNA containing mismatches still remains unclear.We assumed that further elucidating of the kinetics in mismatched sequences can lead to the discrimination of the DNA single-base mismatch based on the kinetics.In this study, we investigated the detailed kinetics of the CT through DNA containing mismatches and tried to discriminate a mismatch sequence based on the kinetics of the CT in DNA containing a mismatch.

View Article: PubMed Central - PubMed

Affiliation: The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki Osaka 567-0047, Japan.

ABSTRACT
Charge transfer (CT) in DNA offers a unique approach for the detection of a single-base mismatch in a DNA molecule. While the single-base mismatch would significantly affect the CT in DNA, the kinetic basis for the drastic decrease in the CT efficiency through DNA containing mismatches still remains unclear. Recently, we determined the rate constants of the CT through the fully matched DNA, and we can now estimate the CT rate constant for a certain fully matched sequence. We assumed that further elucidating of the kinetics in mismatched sequences can lead to the discrimination of the DNA single-base mismatch based on the kinetics. In this study, we investigated the detailed kinetics of the CT through DNA containing mismatches and tried to discriminate a mismatch sequence based on the kinetics of the CT in DNA containing a mismatch.

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Kinetic model for GT-1, M1-C, M1-T, M2-C, M2-T, rs1963939-C and rs1963939-T. Rate constants for CT between Gs were depicted. The values of rate constants were summarized in Table 1 and Supplementary Table S1. Rate constants for inter-strand CT from G to G-containing G/T mismatch across the A/T base pair (kGT-1), across the T/A base pair (kGT-2), CT from G-containing G/T mismatch to G across the A/T base pair (kx), across the T/A base pair (ky), CT between G's through GC repeats (kGC), CT from G (nearest to PTZ) to PTZ (k1). Rate constants for intra-strand CT from G-containing mismatch to G (kGT-6) across T/A, and CT from G-containing mismatch to G across T/A (kGT-7), which is described in Supplementary Figure S11. Explanation for other rate constants is summarized in Supplementary Table S1.
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Figure 3: Kinetic model for GT-1, M1-C, M1-T, M2-C, M2-T, rs1963939-C and rs1963939-T. Rate constants for CT between Gs were depicted. The values of rate constants were summarized in Table 1 and Supplementary Table S1. Rate constants for inter-strand CT from G to G-containing G/T mismatch across the A/T base pair (kGT-1), across the T/A base pair (kGT-2), CT from G-containing G/T mismatch to G across the A/T base pair (kx), across the T/A base pair (ky), CT between G's through GC repeats (kGC), CT from G (nearest to PTZ) to PTZ (k1). Rate constants for intra-strand CT from G-containing mismatch to G (kGT-6) across T/A, and CT from G-containing mismatch to G across T/A (kGT-7), which is described in Supplementary Figure S11. Explanation for other rate constants is summarized in Supplementary Table S1.

Mentions: The rate constants of the single-step CT between G bases (kht) were determined from kinetic modeling. Analysis of time profiles based on the multistep hopping mechanism was performed with numerical analysis by using Matlab software (23). Kinetic model of multistep CT process is shown in Figure 3. Charge recombination process can be ignored because the charge separated state persists over hundred microseconds when NI and the nearest G are separated by six or five A–T base pairs (Figures S2, S3 and S4). According to Figure 3, example simultaneous differential equations for DNAs described in Figure 1a are shown as Equation (1).1where [Gi] (i = 1 ∼ n) and [PTZ] correspond to the charge population at G and PTZ sites, respectively, ks is the CT rate constant between Gs except for k1 which is the rate constants for the CT from G5 to PTZ (23).Figure 1.


Kinetics of charge transfer in DNA containing a mismatch.

Osakada Y, Kawai K, Fujitsuka M, Majima T - Nucleic Acids Res. (2008)

Kinetic model for GT-1, M1-C, M1-T, M2-C, M2-T, rs1963939-C and rs1963939-T. Rate constants for CT between Gs were depicted. The values of rate constants were summarized in Table 1 and Supplementary Table S1. Rate constants for inter-strand CT from G to G-containing G/T mismatch across the A/T base pair (kGT-1), across the T/A base pair (kGT-2), CT from G-containing G/T mismatch to G across the A/T base pair (kx), across the T/A base pair (ky), CT between G's through GC repeats (kGC), CT from G (nearest to PTZ) to PTZ (k1). Rate constants for intra-strand CT from G-containing mismatch to G (kGT-6) across T/A, and CT from G-containing mismatch to G across T/A (kGT-7), which is described in Supplementary Figure S11. Explanation for other rate constants is summarized in Supplementary Table S1.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2553589&req=5

Figure 3: Kinetic model for GT-1, M1-C, M1-T, M2-C, M2-T, rs1963939-C and rs1963939-T. Rate constants for CT between Gs were depicted. The values of rate constants were summarized in Table 1 and Supplementary Table S1. Rate constants for inter-strand CT from G to G-containing G/T mismatch across the A/T base pair (kGT-1), across the T/A base pair (kGT-2), CT from G-containing G/T mismatch to G across the A/T base pair (kx), across the T/A base pair (ky), CT between G's through GC repeats (kGC), CT from G (nearest to PTZ) to PTZ (k1). Rate constants for intra-strand CT from G-containing mismatch to G (kGT-6) across T/A, and CT from G-containing mismatch to G across T/A (kGT-7), which is described in Supplementary Figure S11. Explanation for other rate constants is summarized in Supplementary Table S1.
Mentions: The rate constants of the single-step CT between G bases (kht) were determined from kinetic modeling. Analysis of time profiles based on the multistep hopping mechanism was performed with numerical analysis by using Matlab software (23). Kinetic model of multistep CT process is shown in Figure 3. Charge recombination process can be ignored because the charge separated state persists over hundred microseconds when NI and the nearest G are separated by six or five A–T base pairs (Figures S2, S3 and S4). According to Figure 3, example simultaneous differential equations for DNAs described in Figure 1a are shown as Equation (1).1where [Gi] (i = 1 ∼ n) and [PTZ] correspond to the charge population at G and PTZ sites, respectively, ks is the CT rate constant between Gs except for k1 which is the rate constants for the CT from G5 to PTZ (23).Figure 1.

Bottom Line: While the single-base mismatch would significantly affect the CT in DNA, the kinetic basis for the drastic decrease in the CT efficiency through DNA containing mismatches still remains unclear.We assumed that further elucidating of the kinetics in mismatched sequences can lead to the discrimination of the DNA single-base mismatch based on the kinetics.In this study, we investigated the detailed kinetics of the CT through DNA containing mismatches and tried to discriminate a mismatch sequence based on the kinetics of the CT in DNA containing a mismatch.

View Article: PubMed Central - PubMed

Affiliation: The Institute of Scientific and Industrial Research, Osaka University, Mihogaoka 8-1, Ibaraki Osaka 567-0047, Japan.

ABSTRACT
Charge transfer (CT) in DNA offers a unique approach for the detection of a single-base mismatch in a DNA molecule. While the single-base mismatch would significantly affect the CT in DNA, the kinetic basis for the drastic decrease in the CT efficiency through DNA containing mismatches still remains unclear. Recently, we determined the rate constants of the CT through the fully matched DNA, and we can now estimate the CT rate constant for a certain fully matched sequence. We assumed that further elucidating of the kinetics in mismatched sequences can lead to the discrimination of the DNA single-base mismatch based on the kinetics. In this study, we investigated the detailed kinetics of the CT through DNA containing mismatches and tried to discriminate a mismatch sequence based on the kinetics of the CT in DNA containing a mismatch.

Show MeSH